TSFAE24B

Overall Summary of Treatment-emergent Adverse Events by Toxicity Grade

Output

Code
# Program Name:              tsfae24b.R

# Prep environment:

library(envsetup)
library(tern)
library(dplyr)
library(rtables)
library(junco)

# Define script level parameters:

tblid <- "TSFAE24b"
fileid <- tblid
popfl <- "SAFFL"
trtvar <- "TRT01A"
exclude_G5_if_none <- FALSE
tab_titles <- get_titles_from_file(input_path = '../../_data/', tblid)
string_map <- default_str_map

# Process data:

adsl <- pharmaverseadamjnj::adsl %>%
  filter(!!rlang::sym(popfl) == "Y") %>%
  create_colspan_var(
    non_active_grp = "Placebo",
    non_active_grp_span_lbl = " ",
    active_grp_span_lbl = "Active Study Agent",
    colspan_var = "colspan_trt",
    trt_var = trtvar
  ) %>%
  select(USUBJID, !!rlang::sym(trtvar), colspan_trt)

adae <- pharmaverseadamjnj::adae %>%
  filter(TRTEMFL == "Y") %>%
  mutate(
    ATOXGR = factor(
      ifelse(is.na(AETOXGR), "Missing", paste("Grade", as.character(AETOXGR))),
      levels = c(
        "Grade 5",
        "Grade 4",
        "Grade 3",
        "Grade 2",
        "Grade 1",
        "Missing"
      )
    )
  ) %>%
  select(USUBJID, TRTEMFL, ATOXGR)

ae <- inner_join(adae, adsl, by = c("USUBJID"))

# Keep maximum toxicity per subject.
ae <- ae %>%
  arrange(USUBJID, ATOXGR) %>%
  group_by(USUBJID) %>%
  slice(1) %>%
  ungroup()

# Define layout and build table:

extra_args_1 <- list(.stats = c("count_unique_fraction"))

colspan_trt_map <- create_colspan_map(
  adsl,
  non_active_grp = "Placebo",
  non_active_grp_span_lbl = " ",
  active_grp_span_lbl = "Active Study Agent",
  colspan_var = "colspan_trt",
  trt_var = trtvar
)

lyt <- basic_table(
  show_colcounts = TRUE,
  colcount_format = "N=xx",
  top_level_section_div = " "
) %>%
  append_topleft("n (%)") %>%
  split_cols_by(
    "colspan_trt",
    split_fun = trim_levels_to_map(map = colspan_trt_map)
  ) %>%
  split_cols_by(trtvar) %>%
  analyze_num_patients(
    vars = "USUBJID",
    .stats = "unique",
    .formats = c("unique" = jjcsformat_count_fraction),
    .labels = "Subjects with >= 1 AE"
  ) %>%
  analyze(
    "ATOXGR",
    afun = a_freq_j,
    extra_args = extra_args_1,
    var_labels = "Toxicity grade",
    nested = FALSE,
    show_labels = "visible",
  )


result <- build_table(lyt, ae, alt_counts_df = adsl)

# Prune missing category if all zeros:

if (exclude_G5_if_none == TRUE) {
  result <- safe_prune_table(
    result,
    prune_func = count_pruner(cat_include = c("Grade 5", "Missing"))
  )
} else {
  result <- safe_prune_table(
    result,
    prune_func = count_pruner(cat_include = c("Missing"))
  )
}

# Add titles and footnotes:

result <- set_titles(result, tab_titles)

# Convert to tbl file and output table:

tt_to_tlgrtf(string_map = string_map, tt = result, file = fileid)

TSFAE24b: Overall Summary of [Treatment-emergent Adverse Events] by Toxicity Grade; Safety Analysis Set (Study jjcs - core)

Active Study Agent

Xanomeline High Dose

Xanomeline Low Dose

Placebo

n (%)

N=53

N=73

N=59

Subjects with ≥ 1 AE

51 (96.2%)

62 (84.9%)

42 (71.2%)

Toxicity grade

Grade 5

34 (64.2%)

32 (43.8%)

25 (42.4%)

Grade 4

10 (18.9%)

16 (21.9%)

4 (6.8%)

Grade 3

4 (7.5%)

4 (5.5%)

6 (10.2%)

Grade 2

3 (5.7%)

6 (8.2%)

3 (5.1%)

Grade 1

0

1 (1.4%)

3 (5.1%)

Note: The worst toxicity event experienced by the subject is used. If a subject has all adverse events with missing toxicities, the subject is only counted as missing.

Note: Toxicity grade is evaluated according to NCI-CTCAE version 5.0..

Download RTF file